Variant report

Variant	rs11212525
Chromosome Location	chr11:108016014-108016015
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:108010714-108016397	K562	blood:	n/a	n/a
2	POLR2A	chr11:108015948-108016263	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:108008133..108010844-chr11:108015836..108019565,3	K562	blood:
2	chr11:108013954..108016256-chr11:108494124..108496798,2	K562	blood:
3	chr11:108011494..108013707-chr11:108014897..108016452,2	K562	blood:

Variant related genes	Relation type
ACAT1	TF binding region
ENSG00000075239	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11212484	0.87[CEU][hapmap]
rs11212551	0.86[JPT][hapmap]
rs11605442	0.89[JPT][hapmap]
rs12360727	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12575358	0.81[ASN][1000 genomes]
rs12786416	0.81[AMR][1000 genomes]
rs12787445	0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12794010	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519073	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1550609	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1607476	0.81[JPT][hapmap]
rs183459	0.86[JPT][hapmap]
rs183460	0.86[JPT][hapmap]
rs1850730	0.86[JPT][hapmap]
rs2056267	0.84[JPT][hapmap]
rs2070661	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2083707	0.86[JPT][hapmap]
rs228589	0.86[JPT][hapmap]
rs34971817	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736509	0.83[CEU][hapmap]
rs3781868	0.90[JPT][hapmap]
rs4028262	0.87[CEU][hapmap]
rs4623864	0.86[JPT][hapmap]
rs4754299	0.85[ASN][1000 genomes]
rs4754305	0.86[JPT][hapmap]
rs609557	0.86[JPT][hapmap]
rs609655	0.94[LWK][hapmap]
rs6589007	0.86[JPT][hapmap]
rs7118967	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs7931681	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1039549	chr11:107950572-108034548	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1040522	chr11:107969357-108049672	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11212525	RP11-144G7.2	cis	Muscle Skeletal	GTEx
rs11212525	NPAT	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107993200-108018600	Weak transcription	Thymus	Thymus
2	chr11:107993200-108021800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:107993200-108030000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:107993200-108069600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:107993400-108017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:107993600-108018800	Weak transcription	Fetal Kidney	kidney
7	chr11:107994000-108029600	Weak transcription	Fetal Brain Male	brain
8	chr11:107995000-108018600	Weak transcription	Hela-S3	cervix
9	chr11:107995600-108017800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:107996000-108021400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:107996200-108019200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:108002200-108069600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:108002400-108040200	Strong transcription	Liver	Liver
14	chr11:108002800-108024800	Strong transcription	Fetal Muscle Leg	muscle
15	chr11:108002800-108027000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:108002800-108027200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr11:108002800-108048000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr11:108003000-108018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:108003600-108040800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:108004000-108022000	Strong transcription	Brain Hippocampus Middle	brain
21	chr11:108004200-108035000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr11:108004400-108017800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:108004400-108037600	Strong transcription	Adipose Nuclei	Adipose
24	chr11:108004800-108018600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:108005800-108040800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr11:108006600-108022800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:108006800-108023800	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:108007000-108020600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr11:108007400-108033600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:108007600-108023000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:108007800-108022400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:108007800-108032000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:108008200-108018000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:108008200-108023000	Strong transcription	Fetal Stomach	stomach
35	chr11:108008600-108031200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:108009000-108022800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:108009000-108041000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:108009200-108033400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:108009200-108071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:108009400-108016600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:108009400-108018800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:108009400-108022400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:108009400-108023200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:108009400-108028000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:108009400-108031200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr11:108009400-108040400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:108009400-108062600	Strong transcription	Primary T cells from cord blood	blood
48	chr11:108009400-108068400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:108009600-108023000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:108009600-108023000	Strong transcription	Brain Anterior Caudate	brain

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